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java.lang.Objectuk.ac.sanger.psu.gfmerge.util.debug.Debug
public class Debug
class which contains debugging methods. Logging can be done seperately, on different levels or as a whole.
Field Summary | |
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(package private) static int |
debug_202_1
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(package private) static int |
debug_202_2
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Constructor Summary | |
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Debug()
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Method Summary | |
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static void |
debug_101(int debug,
SimpleArg allArguments)
Debugging Command line arguments Debugging mode 101 - pre processing - |
static void |
debug_102_1(int debug,
java.util.ArrayList gPredicter)
Debugging GenePredicter and Prediction objects Debugging mode 102 - pre processing - |
static void |
debug_102_2(int debug,
java.lang.String gPredictionName,
java.lang.String fName)
Debug Prediction objects in GFMerge Debugging mode 102 - pre processing - |
static void |
debug_102_3(int debug,
java.util.ArrayList predictions)
Debug GeneModel objects in GFMerge Debugging mode 102 - pre processing - |
static void |
debug_103(int debug,
java.lang.String calledByClass,
MyTreeMap tMap)
Debugging MyTreeMap for GMs and Blast hits Debugging mode 103 - pre processing - |
static void |
debug_104(int debug,
java.util.ArrayList arrListOfRegions,
MyTreeMap tMap)
Debugging regions of gene models Debugging mode 104 - pre processing - |
static void |
debug_105(int debug,
java.lang.String calledByClass,
MyTreeMap tMap)
Debugging MyTreeMap for cDNA hits Debugging mode 105 - pre processing - |
static void |
debug_106(int debug,
java.lang.String callingClass,
java.util.ArrayList arrListOfRegions,
MyTreeMap tMap)
Debugging regions of cDNA/Blast hits Debugging mode 106 - pre processing - |
static void |
debug_201(int debug,
java.util.HashMap hashCDnaOverlappedGms)
Debugging hash of by cDNAs overlapped gms Debugging mode 201 - cDNA splice site - |
static void |
debug_202(int debug,
GeneModel gm,
boolean isMinPosTree,
MyTreeMap positionTree)
Debugging CDnaSpliceSite - PostionTree Debugging mode 202 - cDNA splice site - |
static void |
debug_203(int debug,
java.lang.String callingClass,
java.util.HashMap cDnaScoredHash)
Debugging hash of cDNA scored gms Debugging mode 203 - cDNA splice site - |
static void |
debug_204(int debug,
java.lang.String callingClass,
java.util.HashMap highScoringHash)
Debugging hash of high scoring path Debugging mode 204 - cDNA splice site - |
static void |
debug_205(int debug,
java.util.ArrayList arrListOfGmRegs)
Debugging cleaned array of gm regions without lowscoring gms Debugging mode 205 - cDNA splice site - |
static void |
debug_301(int debug,
java.lang.String callingClass,
java.util.HashMap cDnaScoredHash)
Debugging HashMap of genemodels pointing to total feature overlap Debugging mode 301 (203) - cDNA overlap - |
static void |
debug_302(int debug,
java.lang.String callingClass,
java.util.HashMap cDnaScoredHash)
Debugging hash of cDNA overlap scored gms Debugging mode 302 (203) - cDNA overlap - |
static void |
debug_401(int debug,
java.lang.String callingClass,
java.util.HashMap hashFeatOverlappedGms)
Debugging HashMap of gms pointing to array of overlapping features Debugging mode 401 - Blast overlap - |
static void |
debug_402(int debug,
java.lang.String callingClass,
java.util.HashMap hashFeatOverlappedExons)
Debugging HashMap of exons pointing to array of overlapping features Debugging mode 402 - Blast overlap - |
static void |
debug_403(int debug,
GeneModel gm,
java.util.HashMap proteinHash)
Debugging HashMap protein hash for a single gene model Debugging mode 403 - Blast overlap - |
static void |
debug_404(int debug,
GeneModel gm,
java.util.HashMap proteinOverlapLength)
Debugging HashMap of proteins pointing to overlap length Debugging mode 404 - Blast overlap - |
static void |
debug_405(int debug,
GeneModel gm,
java.lang.String proteinID,
long gmLongestOverlap)
Debugging length of longest protein overlap of single gm Debugging mode 405 - Blast overlap - |
static void |
debug_501(int debug,
java.util.HashMap scoredGmHash)
Debugging hash of by equality scored gene models Debugging mode 501 |
static void |
debug_701(int debug,
java.lang.String callingClass,
java.util.ArrayList analyzedGms)
Debugging array of analyzed genemodels Debugging mode 701 - general debugging - |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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static int debug_202_1
static int debug_202_2
Constructor Detail |
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public Debug()
Method Detail |
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public static void debug_101(int debug, SimpleArg allArguments)
debug
- allArguments
- public static void debug_102_1(int debug, java.util.ArrayList gPredicter)
debug
- gPredicter
- public static void debug_102_2(int debug, java.lang.String gPredictionName, java.lang.String fName)
debug
- gPredictionName
- fName
- public static void debug_102_3(int debug, java.util.ArrayList predictions)
debug
- predictions
- public static void debug_103(int debug, java.lang.String calledByClass, MyTreeMap tMap)
debug
- calledByClass
- tMap
- public static void debug_104(int debug, java.util.ArrayList arrListOfRegions, MyTreeMap tMap)
debug
- arrListOfRegions
- tMap
- public static void debug_105(int debug, java.lang.String calledByClass, MyTreeMap tMap)
debug
- calledByClass
- tMap
- public static void debug_106(int debug, java.lang.String callingClass, java.util.ArrayList arrListOfRegions, MyTreeMap tMap)
debug
- callingClass
- arrListOfRegions
- tMap
- public static void debug_201(int debug, java.util.HashMap hashCDnaOverlappedGms)
debug
- hashCDnaOverlappedGms
- public static void debug_202(int debug, GeneModel gm, boolean isMinPosTree, MyTreeMap positionTree)
debug
- gm
- isMinPosTree
- positionTree
- public static void debug_203(int debug, java.lang.String callingClass, java.util.HashMap cDnaScoredHash)
debug
- callingClass
- cDnaScoredHash
- public static void debug_204(int debug, java.lang.String callingClass, java.util.HashMap highScoringHash)
debug
- callingClass
- highScoringHash
- public static void debug_205(int debug, java.util.ArrayList arrListOfGmRegs)
debug
- arrListOfGmRegs
- public static void debug_301(int debug, java.lang.String callingClass, java.util.HashMap cDnaScoredHash)
debug
- callingClass
- cDnaScoredHash
- public static void debug_302(int debug, java.lang.String callingClass, java.util.HashMap cDnaScoredHash)
debug
- callingClass
- cDnaScoredHash
- public static void debug_401(int debug, java.lang.String callingClass, java.util.HashMap hashFeatOverlappedGms)
debug
- callingClass
- hashFeatOverlappedGms
- public static void debug_402(int debug, java.lang.String callingClass, java.util.HashMap hashFeatOverlappedExons)
debug
- callingClass
- hashFeatOverlappedExons
- public static void debug_403(int debug, GeneModel gm, java.util.HashMap proteinHash)
debug
- gm
- proteinHash
- public static void debug_404(int debug, GeneModel gm, java.util.HashMap proteinOverlapLength)
debug
- gm
- proteinOverlapLength
- public static void debug_405(int debug, GeneModel gm, java.lang.String proteinID, long gmLongestOverlap)
debug
- gm
- proteinID
- gmLongestOverlap
- public static void debug_501(int debug, java.util.HashMap scoredGmHash)
debug
- scoredGmHash
- public static void debug_701(int debug, java.lang.String callingClass, java.util.ArrayList analyzedGms)
debug
- callingClass
- analyzedGms
-
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